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Sample GSM3904601 Query DataSets for GSM3904601
Status Public on Jun 28, 2019
Title RNA-seq, RPE, CRISPRa, ctrl, rep1 [4861_1_CM1502_CGATGTA]
Sample type SRA
 
Source name RNA-seq_RPE_CRISPRa_ctrl
Organism Homo sapiens
Characteristics cell line: RPE-1
genotype/variation: stably expressing SunTag-CRISPRa
transfected protein: ctrl
Treatment protocol sgRNAs were cloned into Lentiguide-Puro vector (Addgene #52963) using restriction enzyme BsmBI, and Lentivirus was prepared. RPE-1 cells stably expressing SunTag-CRISPRa were infected with LentiGuide virus and selected with 10 µg/µl Puromycin for one week to obtain stable polyclonal cell pools.
Growth protocol Cells were cultured according to 4DNucleome SOP, https://www.4dnucleome.org/cell-lines.html
Extracted molecule polyA RNA
Extraction protocol total RNA was extracted using TRIsure and selected for polyadenylated fraction
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 4861_1_CM1502_CGATGTA_S2
Data processing Reads were aligned to hg19 using TopHat version 2.1, with Ensembl genome build 75.
Genome_build: GRCh37.75
 
Submission date Jun 25, 2019
Last update date Jun 28, 2019
Contact name Bas van Steensel
E-mail(s) b.v.steensel@nki.nl
Phone + 31 20 512 2040
Fax +31 20 669 1383
URL http://www.nki.nl/nkidep/vansteensel
Organization name Netherlands Cancer Institute
Department division of Molecular Biology
Lab van Steensel group
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
 
Platform ID GPL16791
Series (2)
GSE133273 Effects of transcription on genome - nuclear lamina interactions: RNA-seq data
GSE133275 Effects of transcription on genome - nuclear lamina interactions
Relations
BioSample SAMN12136052
SRA SRX6366102

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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